November 2012 - modeller_usage

scoring function and optimization
by sdimicco 11 Dec '12

11 Dec '12

Dear Modellers, I have three points to discuss. 1) As I changed the optimization protocol, I woul dlike to check if my set up has been done. Where could I check it? 2) I am building a multimeric protein. The DOPE and GA341 scores are developed for single chain models. How can I asses the quality of my models? The sole molpdf is sufficient? 3) I found thie messagge in the log file: Treating residue type GSH as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. I have understood that the input PDB file is the .ini, which is written during the calculation. Thus, how can I "remove the corresponding 'MODELLER BLK RESIDUE" to treat the residue flexible? Have I to define it as my own residue? Thank you in advance All the best Simone

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Regarding Salign Constructed Matrix
by Ashish Runthala 11 Dec '12

11 Dec '12

Dear Modellers, Whenever the SAlign is implemented with a set of templates, it generates a matrix showing some mutual similarity of templates (pairwise equivalences), something like this (against the target with 326 residues). 1SMQA 1H0OA 1SMQA 0 168 1H0OA 0 0 Now, answer me a set of queries. 1. Is 168 showing the count of similar residues, falling within the specified RMSD threshold? 2. Is this calculation considering LGA algorithm? 3. As there are certain folds existing in every such alignment, is there any lower limit of the existing residues in every such chunk to be considered similar. Like, if a fold is more than 3 residues long, i will take it similar in the matrix, and thus i would leave all the nuclear aligned residues. Is it considered this way in the program? Best, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Tuesday, November 20, 2012 9:54:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 109 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: Modeller Help (Modeller Caretaker) 2. optimization protocol and HETATM flexibility (sdimicco) 3. Error while running compare.py (Anogna) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Nov 2012 13:15:30 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> To: mario rossi <sanzodenzel(a)yahoo.it> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] Modeller Help Message-ID: <50AAA172.6070202(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/19/2012 05:59 AM, mario rossi wrote: > I'am Simone an italian student, ineed to learn to use modeller to do > homology modelingbut i have some trouble. > I downloaded and installed both modeller and python on my pc (windows > 7). To learn what to do I tried to follow the basic tutorial but I find > serious problems in giving the input. I can not even load the sequence > as the file (.ali) is not recognized by python and if the command is > entered manually, I get syntax error?? Can you help me to understand > where is the mistake? It's difficult to know what the problem is without a clearer description of what you did, and what results you got. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Tue, 20 Nov 2012 15:32:18 +0100 From: sdimicco <sdimicco(a)unisa.it> To: <modeller_usage(a)salilab.org> Subject: [modeller_usage] optimization protocol and HETATM flexibility Message-ID: <6dfdf81fe2a43f4c7bb0d6c96c07e6d5(a)unisa.it> Content-Type: text/plain; charset="utf-8" Dear Modellers, I am tring to set up my script to build a multimeric model with loop refinement. The script looks like: log.verbose() class dope_loopmodel(dope_loopmodel): def special_patches(self, aln): # Rename both chains and renumber the residues in each self.rename_segments(segment_ids=['A', 'B'], renumber_residues=[1, 1]) env = environ() env.io.hetatm = True a = dope_loopmodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 2 # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 2 a.max_molpdf = 1e6 a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() automodel.final_malign3d = True It seems that the script works but I would like to check if all optimization steps have been done. How could I check it? Please, if you note errors in the script, give me suggestions Moreover, I built a model with an HETATM residue. If I want to treat it as flexible residue: how could I do that? Thank you in advance. Bests Simone

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scoring function and optimization
by sdimicco 26 Nov '12

26 Nov '12

Dear Modellers, I have three points to discuss. 1) As I changed the optimization protocol, I woul dlike to check if my set up has been done. Where could I check it? 2) I am building a multimeric protein. The DOPE and GA341 scores are developed for single chain models. How can I asses the quality of my models? The sole molpdf is sufficient? 3) I found thie messagge in the log file: Treating residue type GSH as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. I have understood that the input PDB file is the .ini, which is written during the calculation. Thus, how can I "remove the corresponding 'MODELLER BLK RESIDUE" to treat the residue flexible? Have I to define it as my own residue? Thank you in advance All the best Simone

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(no subject)
by Shota Nakamura 20 Nov '12

20 Nov '12

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Error while running compare.py
by Anogna 20 Nov '12

20 Nov '12

Dear Modeller Users, I trying simple modelling methodology to model required protein structure. Till build_profile.py everything went well. But when gave compare.py.....i am get an error as follows *Traceback (most recent call last):* * File "compare.py", line 11, in ?* * m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) * * File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 72, in __in* *it__* * self.read(**vars)* * File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 117, in rea* *d* * model_format, model_segment)* *IOError: pdbnam_____E> Filename for PDB code not found: 3d3l* * Directories: .;atom_files* * Extensions : ;.atm;.pdb;.ent;.crd* * (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, * * and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent)* Do I need make any modifications in my compare.py file....I am attaching compare.py file which i used. Please help me with this problem. Thanking You, Anogna

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optimization protocol and HETATM flexibility
by sdimicco 20 Nov '12

20 Nov '12

Dear Modellers, I am tring to set up my script to build a multimeric model with loop refinement. The script looks like: log.verbose() class dope_loopmodel(dope_loopmodel): def special_patches(self, aln): # Rename both chains and renumber the residues in each self.rename_segments(segment_ids=['A', 'B'], renumber_residues=[1, 1]) env = environ() env.io.hetatm = True a = dope_loopmodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 2 # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 2 a.max_molpdf = 1e6 a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() automodel.final_malign3d = True It seems that the script works but I would like to check if all optimization steps have been done. How could I check it? Please, if you note errors in the script, give me suggestions Moreover, I built a model with an HETATM residue. If I want to treat it as flexible residue: how could I do that? Thank you in advance. Bests Simone

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Modeller Help
by mario rossi 19 Nov '12

19 Nov '12

Hello everyone I'am Simone an italian student, ineed to learn to use modeller to do homology modelingbut i have some trouble. I downloaded and installed both modeller and python on my pc (windows 7). To learn what to do I tried to follow the basic tutorial but I find serious problems in giving the input. I can not even load the sequence as the file (.ali) is not recognized by python and if the command is entered manually, I get syntax error?? Can you help me to understand where is the mistake?

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multimeric model and loop refinement
by sdimicco 16 Nov '12

16 Nov '12

Dear Member, I am trying to built a multimeric model. I would like to if I have to use restraints symmetry to model it. Moreover, i would like to built a model with all hydrogens and to refine loop automatically. How can I do that? I am trying to use allh model and loop model in the same script, but without success. Thank you in advance Simone

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Re: [modeller_usage] Introduction of Zinc restraints
by flavio seixas 06 Nov '12

06 Nov '12

Hi Mehdi I never used the restrains you listed before. I can not say if it is right or not. You may try to modeller and see the results by overlaying model and template (SSM superpose) in a graphic software like Coot. My suggestion was more simple. I suggest you modify your alignment file. You may have a lot of identical residues in the alignment of zinc finger region. Try to modeller them as rigid bodies, replacing then in your sequence by dots "." This will copy the restrains of your template to your model. Another suggestion is to do as Ben advised. Regards, Flavio --- On Tue, 11/6/12, Mehdi Talebzadeh Farooji <mahditzf(a)yahoo.com> wrote: From: Mehdi Talebzadeh Farooji <mahditzf(a)yahoo.com> Subject: Re: [modeller_usage] Introduction of Zinc restraints To: "flavio seixas" <oivalf_nix(a)yahoo.com> Date: Tuesday, November 6, 2012, 2:29 AM Hi Flavio Thank you for your reply. I have to sets of restraints, the distance between SG of Cysteins and Zn 2.3 A, ND1 of his and Zn 2.0 A. I intruduced these restraints in MyModel.py class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('SG:204:B', 'ZN:238:B'), ('SG:207:B', 'ZN:238:B'), ('SG:225:B', 'ZN:238:B'), ('ND1:228:B', 'ZN:238:B')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=2.3, stdev=0.03) I am not sure if I am doing right thing. Regards, Mehdi From: flavio seixas <oivalf_nix(a)yahoo.com> To: mahditzf(a)yahoo.com Sent: Sunday, November 4, 2012 9:07:58 PM Subject: Re: [modeller_usage] Introduction of Zinc restraints Hi. try to build identical residues of zinc finger as well zinc atom as rigid bodies "." and modeler only the different residues. Regards flavio ------------------------------ Em sex, 2 de nov de 2012 18:41 GMT Mehdi Talebzadeh Farooji escreveu: >Dear Users, > >I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated. > >Mehdi

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Introduction of Zinc restraints
by Mehdi Talebzadeh Farooji 06 Nov '12

06 Nov '12

Dear Users, I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated. Mehdi

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